-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Jeorge,
the 'ghost' could be explained by a shift of an entire section, i.e. you have to split several residues into A+B, not only the MET. The cylR2 structure in 2XJ3 is one example where this was necessary. Best, Tim On 11/12/2014 11:23 AM, Eleanor Dodson wrote: > That looks really odd - the whole MET has a negative/positive > ghost > > > Second conformations usually branch at the CB, and dont look like > that. > > Are you sure you havent somehow got two MET residues in the > coordinate set ? Turn on cysmmetry display in coot and look for > clashes around there. > > Does the rest of the map look OK? > > I would set the occupancies of the MET and nearby side chains to > 0.00 (you can do that in coot) then refine and look at the maps > again. > > This is very old fashioned but you can do this: distang xyzin > coords.pdb dist inter end > > to get a list of close symmetry clashes & contacts Eleanor > > > On 12 November 2014 09:17, Greg Costakes <[email protected]> > wrote: > >> Hi Jeorge, >> >> The simplest answer is that you have multiple positions for the >> Methionine. So you can try adding in an alternate position for >> it. However, you didn’t mention the sigma cutoff or e-/A^3 for >> either of your density maps. Its quite possible that your fofc >> map is just scaled way down and what you are seeing is an >> exaggeration of what’s barely there. Hope this helps. Cheers! >> >> - Greg >> >> >> ------------------------------------------------------------------------------- >> >> Greg Costakes, Ph.D. >> Department of Biochemistry University of Cambridge 80 Tennis >> Court Road Cambridge, CB2 1GA United Kingdom >> >> -------------------------------------------------------------------------------- >> >> >> *From:* jeorgemarley thomas <[email protected]> >> *Sent:* Wednesday, November 12, 2014 8:16 AM *To:* >> [email protected] *Subject:* [ccp4bb] Refinement with >> refmac05 and methionine density >> >> Dear All, >> >> I am refining the structure with refmac05, and after each >> refinement the density around this methionine is flipping. and it >> is difficult to say where this methionine actually have the >> density. please suggest what I should I do. I am attaching the >> snap here. >> >> Thanks in Advance for your kind suggestions >> >> Jeorge >> >> >> >> >> ------------------------------ <http://www.avast.com/> >> >> This email is free from viruses and malware because avast! >> Antivirus <http://www.avast.com/> protection is active. >> >> > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFUY0O/UxlJ7aRr7hoRArkIAJsHP6gLpSkRtJPEE7/P/R453uGvJACeMfus jFS3EEDy7g7ss5A6L3D3cco= =uLjH -----END PGP SIGNATURE-----
